I spoke to the aspnet IISIntegration team members and found my solution.
tldr: Empty out your wwwroot folder on kudu.
The issue relates to having old things leftover from previous 1.x deployments
Step 1:
Navigate to the Kudu Console (https://{yourapp}.scm.azurewebsites.net/)
Step 2:
Step 3:
(Note: navigate into the "site" directory)
(Note: there is a wwwroot folder within this wwwroot. You should delete the one that is in the "site" directory)
Step 4:
Add a new empty folder called wwwroot where you just deleted the previous one (within "site" directory)
(Note: my deployment failed when I didn't have the empty wwwroot folder in there)
Step 5: Redeploy your app and hopefully it works. Good luck
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